Re: [base] problems with my trashcan
This thread prompted me to figure out why I couldn't empty my BASE2 trashcan.
Some items involved convoluted procedures:
Deleting a user involved undeleting it ('restore' in BASE2 parlance), logging
in as that user, deleting its home directory and default directories, empty
its trashcan, log out, then delete user again as administrator.
I had an annotation type which wasn't deleting. The used item page pointed
just to Annotation [id=] where the link was not functional. I managed
to find which sample was annotated with this annotation type by a similar
process as above - undeleting it, listing all samples matching '%' on this
annotation type in the sample list view.
I'm still stuck with one item which produces a stacktrace (see below). As
with Chad, it could result from some strange/unpredictable user and system
behaviour while installing/using new plugins.
many thanks,
Bob
Here's the problem item:
1. Plugin definitionBatch Data Importer
(Note that I'm not bang up to date.)
Version BASE 2.4.2pre (build #3730; schema #40)
Web server Apache Tomcat/5.5.20
Database Server MySQL 5.0.21-max-log
Database Dialectorg.hibernate.dialect.MySQLInnoDBDialect
JDBC Driver com.mysql.jdbc.Driver (version 5.0)
Java runtimeJava(TM) SE Runtime Environment (1.6.0-b105), Sun Microsystems
Inc.
Operating systemLinux amd64 2.6.16.27-0.9-smp
Memory Total: 230.8 MB
Free: 67.2 MB
Max: 910.3 MB
Browser Mozilla/5.0 (Macintosh; U; Intel Mac OS X; en-US; rv:1.8.1.7)
Gecko/20070914 Firefox/2.0.0.7
Error message Cannot delete or update a parent row: a foreign key constraint
fails (`base2dev/Jobs`, CONSTRAINT `FK23507617401FCE` FOREIGN KEY
(`plugindefinition_id`) REFERENCES `PluginDefinitions` (`id`))
Stack trace
...at HibernateUtil.commit(HibernateUtil.java:910)
...at DbControl.commit(DbControl.java:393)
...at Trashcan.delete(Trashcan.java:229)
...at org.apache.jsp.views.trashcan.index_jsp._jspService(index_jsp.java:139)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334)
...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
...at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
...at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
...at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
...at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:541)
...at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
...at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
...at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
...at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
...at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
...at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
...at java.lang.Thread.run(Thread.java:619)
Caused by: com.mysql.jdbc.exceptions.MySQLIntegrityConstraintViolationException
...at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:931)
...at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2934)
...at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1616)
...at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1708)
...at com.mysql.jdbc.Connection.execSQL(Connection.java:3255)
...at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1293)
...at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1566)
...at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1480)
...at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1465)
...at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105)
...at
Re: [base] problems with my trashcan
Hi Bob,
Looks like there is a Job item that used the batch importer and
therefore you cannot delete the plugin definition while the Job item
still exists. Try deleting that job and it should go.
Cheers
Micha
==
Dr Micha M Bayer
Bioinformatics Specialist
Genetics Programme
The Scottish Crop Research Institute
Invergowrie
Dundee
DD2 5DA
Scotland, UK
Telephone +44(0)1382 562731 ext. 2309
Fax +44(0)1382 562426
http://www.scri.ac.uk/staff/michabayer
==
-Original Message-
From: [EMAIL PROTECTED] [mailto:basedb-users-
[EMAIL PROTECTED] On Behalf Of Bob MacCallum
Sent: 08 October 2007 11:41
To: BASE ML
Subject: Re: [base] problems with my trashcan
This thread prompted me to figure out why I couldn't empty my BASE2
trashcan.
Some items involved convoluted procedures:
Deleting a user involved undeleting it ('restore' in BASE2 parlance),
logging
in as that user, deleting its home directory and default directories,
empty
its trashcan, log out, then delete user again as administrator.
I had an annotation type which wasn't deleting. The used item page
pointed
just to Annotation [id=] where the link was not functional. I
managed
to find which sample was annotated with this annotation type by a
similar
process as above - undeleting it, listing all samples matching '%' on
this
annotation type in the sample list view.
I'm still stuck with one item which produces a stacktrace (see below).
As
with Chad, it could result from some strange/unpredictable user and
system
behaviour while installing/using new plugins.
many thanks,
Bob
Here's the problem item:
1. Plugin definition Batch Data Importer
(Note that I'm not bang up to date.)
Version BASE 2.4.2pre (build #3730; schema #40)
Web serverApache Tomcat/5.5.20
Database Server MySQL 5.0.21-max-log
Database Dialect org.hibernate.dialect.MySQLInnoDBDialect
JDBC Driver com.mysql.jdbc.Driver (version 5.0)
Java runtime Java(TM) SE Runtime Environment (1.6.0-b105), Sun
Microsystems Inc.
Operating system Linux amd64 2.6.16.27-0.9-smp
MemoryTotal: 230.8 MB
Free: 67.2 MB
Max: 910.3 MB
Browser Mozilla/5.0 (Macintosh; U; Intel Mac OS X; en-US;
rv:1.8.1.7)
Gecko/20070914 Firefox/2.0.0.7
Error message Cannot delete or update a parent row: a foreign
key
constraint fails (`base2dev/Jobs`, CONSTRAINT `FK23507617401FCE`
FOREIGN KEY (`plugindefinition_id`) REFERENCES `PluginDefinitions`
(`id`))
Stack trace
...at HibernateUtil.commit(HibernateUtil.java:910)
...at DbControl.commit(DbControl.java:393)
...at Trashcan.delete(Trashcan.java:229)
...at
org.apache.jsp.views.trashcan.index_jsp._jspService(index_jsp.java:139)
...at
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.j
ava:334)
...at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314
)
...at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applic
ationFilterChain.java:252)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFil
terChain.java:173)
...at
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(Char
acterEncodingFilter.java:72)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applic
ationFilterChain.java:202)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFil
terChain.java:173)
...at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVal
ve.java:213)
...at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextVal
ve.java:178)
...at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.jav
a:126)
...at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.jav
a:105)
...at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:54
1)
...at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve
.java:107)
...at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
148)
...at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:8
69)
...at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.pro
cessConnection(Http11BaseProtocol.java:664)
...at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoin
t.java:527)
...at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollo
werWorkerThread.java:80)
...at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPoo
l.java:684)
...at java.lang.Thread.run(Thread.java:619)
Caused by:
